Wiki¶

Tychus installation and pipeline testing¶

Installation¶

Clone the repository or specific branch by

git clone https://github.com/egeza/Tychus.git

git clone -b ilifu https://github.com/egeza/Tychus.git

Inside the Tychus dir fetch all (if you did clone the directory not just a branch) remote branches and check if they are all cloned

git fetch --all
git branch -a

We use ilifu cluster therefore we create a local branch for the ilifu remote branch `git checkout ilifu'

Verify cloned branch is ilifu git branch

Issues and debugging¶

1. kSNP3 - kSNP3 repository doesn't exist anymore as a result, we resorted to getting the singularity images from Katie /cbio/projects/025/images/ , while debugging the pipeline.

2. Prokka image - Struggled with the tbl2asn (now called table2asn), first tried downloading the existing docker image from https://github.com/tseemann/prokka#singularity and https://github.com/tseemann/prokka/issues/453 without success. We then used https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/ as a referral from https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ to build a docker image on BST from a Dockerfile in /home/ephie/Tychus/dockerfiles/docker_prokka.
   Challenge of "no space left on device" on the BST machine was resolved by Gerrit by docker rmi docker_id -f and docker image prune -a -f. We then used the singularityware/docker2singularity to convert docker image to singularity and transferred it to ilifu /cbio/projects/025/images/prokka_latest.simg .
   On ilifu, edit the conf/ilifu_assembly.config file withName: AnnotateContigs{ container='/cbio/users/katie/singularity_containers/prokka.simg' to the correct prokka image. Remember to edit the CacheDir and container if using the images to run the pipeline in the same config file.

3. Alignment module of the pipeline
   When testing the pipeline with tutorial data, we had issues when building indexes from the databases: ecoli virulence and plasmid, make sure that all lines under PATH TO EXTERNAL RESOURCES are commented out except the genome pointing to the reference of ecoli in tutorial

   genome = "$baseDir/tutorial/reference/EcoliK-12MG1655.fa"
   

   Also, accessing the JAVA from ilifu was an issue, thus, so it's best to comment it out in conf/ilifu_alignment.config

   JAVA='/cbio/soft/jdk-11.0.2/bin'
   

   and also remove the variable ${JAVA}/ when running trimmomatic in the alignment.nf file.

Analysis of Lactobacillus iners¶

Reference genome of interest (/cbio/projects/025/Tychus_DBs) e.g.¶

Our reference is the Lactobacillus iners (https://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/Lactobacillus_iners/)